SimpleProfileProfileAligner (biojava 5.2.0 API)
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Field Summary
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Fields inherited from class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
pair
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Fields inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
anchors, cutsPerSection, gapPenalty, max, min, profile, score, scores, time, xyMax, xyStart
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Constructor Summary
Constructors Constructor Description SimpleProfileProfileAligner()Before running a profile-profile alignment, data must be sent in via calls to
AbstractProfileProfileAligner.setQuery(Profile),AbstractProfileProfileAligner.setTarget(Profile),AbstractMatrixAligner.setGapPenalty(GapPenalty), andAbstractMatrixAligner.setSubstitutionMatrix(SubstitutionMatrix).SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Future<ProfilePair<S,C>> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Profile<S,C> query, Future<ProfilePair<S,C>> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)Prepares for a profile-profile alignment run concurrently.
SimpleProfileProfileAligner(Profile<S,C> query, Profile<S,C> target, GapPenalty gapPenalty, SubstitutionMatrix<C> subMatrix)Prepares for a profile-profile alignment.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected voidsetProfile(List<AlignedSequence.Step> sx, List<AlignedSequence.Step> sy)-
Methods inherited from class org.biojava.nbio.alignment.template.AbstractProfileProfileAligner
getCompoundSet, getCompoundsOfQuery, getCompoundsOfTarget, getPair, getQuery, getScoreMatrixDimensions, getSubstitutionScore, getTarget, isReady, reset, setQuery, setTarget
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Methods inherited from class org.biojava.nbio.alignment.template.AbstractMatrixAligner
align, getComputationTime, getGapPenalty, getMaxScore, getMinScore, getProfile, getScore, getScoreMatrix, getScoreMatrixAsString, getSubstitutionMatrix, getSubstitutionScoreVector, getSubstitutionScoreVector, isLocal, isStoringScoreMatrix, setGapPenalty, setStoringScoreMatrix, setSubstitutionMatrix
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Methods inherited from class org.biojava.nbio.alignment.template.AbstractScorer
getDistance, getDistance, getSimilarity, getSimilarity
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.biojava.nbio.alignment.template.Aligner
getComputationTime, getProfile
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Methods inherited from interface org.biojava.nbio.alignment.template.Scorer
getDistance, getDistance, getMaxScore, getMinScore, getScore, getSimilarity, getSimilarity
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